3B50 | pdb_00003b50

Structure of H. influenzae sialic acid binding protein bound to Neu5Ac.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	37 mg/mL SiaP in 20 mM HEPES, 10 mM NaCl, 10 mM Neu5Ac, pH 8.0 and reservoir solution (100 mM MES, 30% w/v PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.527	α = 90
b = 74.598	β = 90
c = 86.534	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2006-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.9793	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.4	36.37	99.6	0.079	10.1	7.03		61154

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4	1.45	96.8		0.494	2.5	5.34	5879

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	36.37	61075	3094	99.57	0.163	0.161	0.1695	0.201	0.1996	RANDOM	15.062

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.12			-0.35		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.023
r_dihedral_angle_3_deg	13.438
r_dihedral_angle_4_deg	9.879
r_dihedral_angle_1_deg	5.69
r_scangle_it	3.802
r_scbond_it	2.91
r_mcangle_it	1.683
r_angle_refined_deg	1.463
r_mcbond_it	1.414
r_angle_other_deg	0.92
r_mcbond_other	0.642
r_chiral_restr	0.238
r_nbd_refined	0.236
r_symmetry_vdw_other	0.207
r_nbtor_refined	0.189
r_nbd_other	0.177
r_symmetry_vdw_refined	0.168
r_symmetry_hbond_refined	0.164
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2471
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	21

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction